Common Definitions and Terms in Organic Chemistry

electronic configuration: the particular order in which electrons are arranged in an atom or molecule. [Used in a distinct and different sense from stereochemical configuration.]

electronic transition: in an atom or molecule the electrons have certain allowed energies only (orbitals). If an electron passes from one orbital to another an electronic transition occurs and there is the emission or absorption of energy corresponding to the difference in energy of the two orbitals.

electrophile: an atom, molecule or ion able to accept an electron pair.

electrophilic substitution: an overall reaction in which an electrophile binds to a substrate with the expulsion of another electrophile. [The most common example is the electrophilic substitution of a proton by another electrophile, such as a nitronium ion, on an aromatic substrate such as benzene.

electrovalent (ionic) bond: bonding by electrostatic attraction.

element: a substance which cannot be further subdivided by chemical methods.

enantiomers: a pair of isomers which are related as mirror images of one another. [E.g. isomers differing only in the configuration about the chiral atoms.]

endothermic: a reaction in which heat is absorbed.

energy diagram (or reaction energy diagram): a graph of the energy of a reaction against the progress of the reaction.

enthalpy: a thermodynamic state function, generally measured in kilojoules per mole. In chemical reactions the enthalpy change (deltaH) is related to changes in the free energy (deltaG) and entropy (deltaS) by the equation:

deltaG = deltaH - T.deltaS

entropy: a thermodynamic quantity which is a measure of the degree of disorder within any system. [The greater the degree of order the higher the entropy; for an increase in entropy S is positive. Entropy has the units of joules per degree K per mole.]

enzyme: a naturally occurring substance able to catalyse a chemical reaction.

epimerization: a process in which the configuration about one chiral centre of a compound, containing more than one chiral atom, is inverted to give the opposite configuration. [The term epimers is often used to describe two related compounds which differ only in the configuration about one chiral atom.]

half-life, t1/2: the time taken for the concentration of a substance in a reaction to reduce to half its original value.

[Used in first order reactions and as a measure of the rate of radioactive decay.]

hard and soft acids and bases: a classification of acids and bases depending on their polarizability. [Hard bases include fluoride ions; soft bases include triphenylphosphine. Hard acids include Na+, whilst an example of a soft, polarisable acid is Pt2+; hard-hard and soft-soft interactions are favoured. Hardness and softness can be described in terms of the HOMO and LUMO interactions.]

heat of reaction: the amount of heat absorbed or evolved when specified amounts of compounds react under constant pressure. [Expressed as kilojoules per mole. For exothermic reactions the convention is that the enthalpy change (heat of reaction) is negative.]

heterogeneous reaction: a reaction which occurs between substances which are mainly present in different phases. [For example, between a gas and a liquid.]

heterolytic reaction: a reaction in which a covalent bond is broken with unequal sharing of the electrons from the bond.

HOMO: the highest occupied molecular orbital of a molecule, ion or atom.

homolytic reaction: a reaction in which a covalent bond is broken with equal sharing of the electrons from the bond.

hybridization: the process whereby atomic orbitals of different type but similar energies are combined to form a set of equivalent hybid orbitals. These hybrid orbitals do not exist in the atoms but only in the formation of molecular orbitals by combining atomic orbitals from different atoms.

hydroboration: the cis-addition of B-H bonds across double (or triple) carbon-carbon bonds.

hydrogenolysis: the cleaving of a chemical bond by hydrogen. [Generally carried out in the presence of a hydrogenation catalyst.]

hydrolysis: the addition of the elements of water to a substance, often with the partition of the substance into two parts, such as in the hydrolysis of an ester to an acid and an alcohol.

inductive effect: an electronic effect transmitted through bonds in an organic compound due to the electronegativity of substituents and the permanent polarization thereof. [The substituent either induces charge towards or away from itself with the formation of a dipole.]

infrared spectroscopy: the study of the absorption of infrared light by substances. [Since this corresponds to vibrational (and some rotational) changes, infrared spectroscopy provides valuable information about the structure of a substance. Detailed correlation tables exist relating infrared bands (absorbances) to functional groups.]

inhibitor: a general term for any compound which will inhibit (slow down) a reaction. [Inhibitors vcan be used to slow down or stop free radical chain reactions.]

ion: an atom or group of atoms that has lost or gained one or more electrons to become a charged species.

isomers: compounds having the same atomic composition (constitution) but differing in their chemical structure. [They include: structural isomers (chain or positional), tautomeric isomers, and stereoisomers - including geometrical isomers, optical isomers and conformational isomers.]

kinetics: the study of the rate of reactions.

kinetically controlled product: the product formed as the result of the fastest reaction in a set of competing reaction pathways.

laevorotatory: the phenomenon that turns plane polarised light in an anticlockwise direction.

LCAO: a method for the calculation of molecular orbitals from a linear combination of atomic orbitals.

Lewis acid: an agent capable of accepoting a pair of electrons to form a coordinate bond.

Lewis base: an agent capable of donating a pair of electrons to form a coordinate bond.

lone pair: a pair of electrons in a molecule which is not shared by two of the constituent atoms.

LUMO: the lowest unoccupied molecular orbital in a molecule or ion.

Markownikow's rule: in the ionic addition of hydrogen halides to a carbon-carbon double bond the halogen attaches itself to the carbon atom bearing the least number of hydrogen atoms.

[The rule is useful in the prediction of the major product from such reactions. Free radical reactions proceed in the opposite sense, giving rise to anti-Markownikow addition.]

mass spectrometry: a form of spectrometry in which, generally, high energy electrons are bombarded onto a sample and this generates charged fragments of the parent substance; these ions are then focused by electrostatic and magnetic fields to give a spectrum of the charged fragments.

mesomerism: = resonance.

protecting group: a group that is used to protect a functional group from unwanted reactions. After application the protecting group can be removed to reveal the original functional group.

racemic mixture, racemate: an equimolar mixture of the two enantiomeric isomers of a compound. [As a consequence of the equal numbers of laevo- and dextro-rotatory molecules present in a racemate, there is no net rotation of plane polarized light.]

radical: a term applied to an atom or molecule having one or more free valencies. [See 'free radicals'.]

reduction: chemical processes in which the proportion of more electronegative substituents is decreased, or the charge is made more negative, or the oxidation number is lowered.

resolution: the separation of a racemate into its two enantiomers by means of some chiral agency.

resonance: the representation of a compound by two or more canonical structures in which the valence electrons are rearranged to give structures of similar probability. [The actual structure is considered to be a hybrid or the resonance forms.]

reversible process: a process in which the forward reaction can

reach an equilibrium with the reverse reaction.

rotamers: isomers formed by restricted rotation. [See also conformational isomers.]

R,S convention: a formal non-ambiguous, nomenclature system for the assignment of absolute configuration of structure to chiral atoms, using the Cahn, Ingold and Prelog priority rules.

saturated: the term given to organic molecules which contain no multiple bonds.

sawhorse projection: the sideways projection of a carbon-carbon single bond and the attached substituents. [It gives a clearer representation of stereochemistry than the Fischer projection. See also Newman projection.]

spectrometer: an instrument that measures the spectrum of a sample. [For example a mass spectrometer]

spectrophotometer: an instrument that measures the degree of absorption (or emission) of electromagnetic radiation by a substance. The measuring system generally includes a photomultiplier. [ U.v., i.r., visible, and microwave regions of the electromagnetic spectrum may be measured in this way.]

stability constant: when a complex is formed between a metal ion and an a ligand in solution, the equilibrium may be expressed by a constant which is related to the free energy change for the process:

For: M + A = MA : - deltaG = RTlnK

stereochemistry: the study of the spatial arrangements of atoms in molecules and complexes.

stereoisomer: another name for configurational isomer.

stereospecific reactions: reactions in which bonds are broken and made at a particular carbon atom and which lead to a single stereoisomer. If the configuration is altered in the process the reaction is said to involve inversion of configuration; if the configuration remains the same the transformation occurs with retention of configuration.

steric hindrance: the phenomenon of physical blockage of a particular site within a molecule by the presence of local atoms or groups of atoms. [As a consequence of steric hindrance, a reaction at a particular site will be impeded.]

structural isomerism: isomers which differ in the order of bonding of the constituent atoms.

substitution reactions: reactions in which one atom or group of atoms is replaced by another atom or group of atoms. [See electrophilic substitutions and nucleophilic substitutions.]

tautomerism: a form of structural isomerism where the two structures are interconvertible by means of the migration of a proton.

tosylation: a reaction which introduces the toluene-4-sulphonyl group into a molecule. [Generally by reaction of an alcohol with tosyl chloride to give the tosylate ester.]

transition state: the point of highest energy on an energy against reaction coordinate curve. [By definition the transition state is the least stable point (peak) on a reaction path; a reaction path may involve more than one transition states.

ultraviolet light: radiation of an energy range than that of visible light but lower than that of ionising radiations such as X-rays. Many substances absorb ultraviolet light, leading to electronic excitation. [This process is useful both as a means for characterising materials and for stimulating chemical reactions (photochemical reactions.)]

unsaturated: the term given to an organic compound containing multiple bonds.

valence isomerisation: the isomerisation of molecules which involve structural changes resulting only from a relocation of single and double bonds. If a dynamic equilibrium is established between the two isomers it is also referred to as valence tautomerism. An example is the valence tautomerism of cyclo-octa-1,3,5-triene.]

valence bond theory: the wave mechanical basis of resonance theory.

vinyl group: the ethenyl group, -CH=CH2.

Walden inversion: a Walden inversion occurs at a tetrahedral carbon atom during an SN2 reaction when the entry of the reagent and the departure of the leaving group are synchronous. The result is an inversion of configuration at the centre under attack.